Rourke, who played a down-on-his-luck professional wrestler named Randy "The Ram" Robinson in the film directed by Darren Aronofsky, received a standing ovation and loud cheers from the audience as he made his way to the stage. "Thank you all very much," he shouted to the crowd as he took the microphone.
In his expletive-laden speech, he also thanked his costar Marisa Tomei, who played an exotic dancer, saying, "Not many girls can climb the pole, and she did it well."
Melissa Leo took home the best female lead award for her performance in "Frozen River" as an impoverished single mother who smuggles illegal immigrants over the Canadian border.
"You know you are my people," Leo said from the podium, addressing an audience of independent-film supporters.
Rounding out the acting categories, Penelope Cruz won best supporting female for her performance in " Vicky Cristina Barcelona," and James Franco won best supporting male for his work in "Milk."
Rourke, Leo and Cruz have also been nominated for Academy Awards for their roles. In past years, several Spirit Award winners have gone on to earn an Oscar for the same performance, including Charlize Theron for "Monster" and Hilary Swank for "Boys Don't Cry."
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Other awards: Best director went to Tom McCarthy for "The Visitor"; best documentary went to James Marsh for "Man on Wire"; best foreign film went to Laurent Cantet for "The Class"; best screenplay went to Woody Allen for "Vicky Cristina Barcelona"; and best first screenplay went to Dustin Lance Black for "Milk."
Margaret Brown ("The Order of Myths") won the Truer than Fiction award, and Heather Rae ("Frozen River," "Ibid") received the producer award.
The Someone to Watch award went to filmmaker Lynn Shelton ("My Effortless Brilliance"), and the John Cassavetes Award, which is given to films made for less than $500,000, was presented to " In Search of a Midnight Kiss."
The second annual Robert Altman Award, given to the film's director, casting director and ensemble cast, was presented to the team behind "Synecdoche, New York," which also won for best first feature for writer-turned-director Charlie Kaufman.
For nearly a quarter of a century, the Spirit Awards have been the cool cousin to tonight's Academy Awards. Attendees at the ceremony, which is held in a large tent near the sand at Santa Monica Beach, will often forgo designer gowns, tuxedos and million-dollar jewels for jeans, comfortable shirts, leather jackets and tennis shoes.
The Spirit Awards celebrate independent, low-budget filmmaking.
Eligible films must be at least 70 minutes long, and the cost of the completed movie -- including any post-production fees -- has to be less than $20 million.
British comic actor Steve Coogan served as host of the two-hour ceremony, which was shown live and uncut on cable's Independent Film Channel.